Today, I have deleted a misbehaving theme and re-installed it. Absolutely nothing else was done. I re-launched RW after that and all my themes, Stacks-plugin and stacks disappeared. I was able to re-install Stacks plugin.
When I look inside:
Group Containers > P97H7FTHWN.com.realmacsoftware.rapidweaver > Library > Application Support > Addons > Stacks
I have and I posted about it not too long ago. Mine disappeared from RW7 when I upload RW8 demo. Had to reload all themes and addons manually. Have not had an issue since.
One day before this happened, I had to re-install my OS. After that, everything worked as normal.
Yesterday, I opened RW and after few minutes decided to re-install a misbehaving theme. It was misbehaving since I installed it couple of weeks ago. I quit RW and deleted the theme (@AAron: directly—from Finder), then re-installed it without an issue. I restarted my Mac. Only when I tried to relaunch RW I got error messages, which I described earlier. I had to also re-install Stacks plugin.
@teefers: Like I said before, the Themes folder is empty, except that one theme I just re-installed. But when I check Addons within RW, all built-in themes are showing. Exactly same with plugins, but stacks panel is empty.
Like Pete, I just re-installed my addons, taking this opportunity to trim off all the superfluous stuff that I have never used. Hopefully, it will work smoothly now. But my puzzlement at why the addons disappeared in the first place is no lesser than before.